The scratch test was conducted for polycarbonate (PC) and poly(methyl methacrylate) (PMMA) with a load-progressive mode. Changes in the molecular aggregation structure of PC and PMMA induced by the scratch test were investigated based on polarized optical microscopic observation and small-angle X-ray scattering (SAXS) measurement. The scratching coefficient of friction (SCOF), the ratio of tangential load to normal load, of PC was much larger than that of PMMA. The width and depth of the damage on the scratch path was increased monotonically with the increase in the normal load. Hardness obtained by nanoindentation and microindentation tests were similar to those with SCOF, indicating that compression resistance mainly governs the scratch properties. The polarized optical microscopic images revealed that molecules were oriented from the edge to the center of the scratch path at a certain acute angle for both PC and PMMA. SAXS measurement revealed that microfibrils were formed along the direction of stress for PC.